Browse Articles

Bacterial motility depends on a critical flagellum length and energy-optimized assembly

The flagellum is the most complex macromolecular structure known in bacteria and is composed of around two dozen distinct proteins. The main building block of the long, external flagellar filament, flagellin, is secreted through the flagellar type-III secretion system at a remarkable rate of several tens of thousands of amino acids per second, significantly surpassing the rates achieved by other pore-based protein secretion systems. The evolutionary implications and potential benefits of this high secretion rate for flagellum assembly and function, however, have remained elusive. In this study, we provide both experimental and theoretical evidence that the flagellar secretion rate has been evolutionarily optimized to facilitate rapid and efficient construction of a functional flagellum. By synchronizing flagellar assembly, we found that a minimal filament length of 2.5 μm was required for swimming motility. Biophysical modeling revealed that this minimal filament length threshold resulted from an elasto-hydrodynamic instability of the whole swimming cell, dependent on the filament length. Furthermore, we developed a stepwise filament labeling method combined with electron microscopy visualization to validate predicted flagellin secretion rates of up to 10,000 amino acids per second. A biophysical model of flagellum growth demonstrates that the observed high flagellin secretion rate efficiently balances filament elongation and energy consumption, thereby enabling motility in the shortest amount of time. Taken together, these insights underscore the evolutionary pressures that have shaped the development and optimization of the flagellum and type-III secretion system, illuminating the intricate interplay and cost-benefit tradeoff between functionality and efficiency in assembly of large macromolecular structures.

Revisiting the soil carbon saturation concept to inform a risk index in European agricultural soils

Abstract The form in which soil organic carbon (SOC) is stored determines its capacity and stability, commonly described by separating bulk SOC into its particulate- (POC) and mineral-associated (MAOC) constituents. MAOC is more persistent, but the association with mineral surfaces imposes a maximum MAOC capacity for a given fine fraction content. Here, we leverage SOC fraction data and spectroscopy to investigate POC/MAOC distribution, together with SOC changes data over 2009–2018 period, across pedo-climatic zones in the European Union and the UK. We find that rather than a universal mineralogy- dependent maximum MAOC capacity, an emergent effective MAOC capacity can be identified across pedo-climatic zones. These findings led us to propose the SOC risk index, combining SOC changes and effective MAOC capacity. We find that between 43 and 83 Mha of agricultural soils are classified as high risk, mostly constrained to cool and humid regions. The index provides a synthetic information to decision makers for preserving and accruing POC and MAOC.

Single image de-raining by multi-scale Fourier Transform network

Removing rain streaks from a single image presents a significant challenge due to the spatial variability of the streaks within the rainy image. While data-driven rain removal algorithms have shown promising results, they remain constrained by issues such as heavy reliance on large datasets and limited interpretability. In this paper, we propose a novel approach for single-image de-raining that is guided by Fourier Transform prior knowledge. Our method utilises inherent frequency domain information to efficiently reduce rain streaks and restore image clarity. Initially, the rainy image is decomposed into its amplitude and phase components using the Fourier Transform, where rain streaks predominantly affect the amplitude component. Following this, data-driven algorithms are employed separately to process the amplitude and phase components. Enhanced features are then reconstructed using the inverse Fourier Transform, resulting in improved clarity. Finally, a multi-scale neural network incorporating attention mechanisms at different scales is applied to further refine the processed features, enhancing the robustness of the algorithm. Experimental results demonstrate that our proposed method significantly outperforms existing state-of-the-art approaches, both in qualitative and quantitative evaluations. This innovative strategy effectively combines the strengths of Fourier Transform and data-driven techniques, offering a more interpretable and efficient solution for single-image de-raining (Code: https://github.com/zhengchaobing/DeRain).

ITGB5 is a prognostic factor in colorectal cancer and promotes cancer progression and metastasis through the Wnt signaling pathway

Initiation of transthyretin aggregation at neutral pH by fluid agitation

The transthyretin (TTR) tetramer, assembled as a dimer of dimers, transports thyroxine and retinol binding protein in blood plasma and cerebrospinal fluid. Aggregation of wild type (WT) or pathogenic variant TTR leads to transthyretin amyloidosis, which is associated with neurodegenerative and cardiac disease. The trigger for TTR aggregation under physiological conditions is unknown. The tetramer is extremely stable at neutral pH, but aggregation via tetramer dissociation and monomer misfolding can be induced in vitro by lowering the pH. To elucidate factors that may cause TTR aggregation at neutral pH, we examined the effect of shear forces such as those that arise from fluid flow in the vascular system. Fluid shear forces were generated by rapidly stirring TTR solutions in conical microcentrifuge tubes. Under agitation, TTR formed β-rich aggregates and fibrils at a rate that was dependent upon protein concentration. The lag time before the onset of agitation-induced aggregation increases as the total TTR concentration is increased, consistent with a mechanism in which the tetramer first dissociates to form monomer that either partially unfolds to enter the aggregation pathway or reassociates to form tetramer. NMR spectra recorded at various time points during the lag phase revealed growth of an aggregation-prone intermediate trapped as a dynamically perturbed tetramer. Enhanced conformational fluctuations in the weak dimer–dimer interface suggest loosening of critical intersubunit contacts which likely destabilizes the agitated tetramer and predisposes it toward dissociation. These studies provide insights into the mechanism of aggregation of WT human TTR under near-physiological conditions.

Real-time label-free imaging of living crystallization-driven self-assembly

Abstract Living crystallization-driven self-assembly (CDSA) of semicrystalline block copolymers is a powerful method for the bottom-up construction of uniform polymer microstructures with complex hierarchies. Improving our ability to engineer such complex particles demands a better understanding of how to precisely control the self-assembly process. Here, we apply interferometric scattering (iSCAT) microscopy to observe the real-time growth of individual poly( ε -caprolactone)-based fibers and platelets. This label-free method enables us to map the role of key reaction parameters on platelet growth rate, size, and morphology. Furthermore, iSCAT provides a contrast mechanism for studying multi-annulus platelets formed via the sequential addition of different unimers, offering insights into the spatial distribution of polymer compositions within a single platelet.

Biochar enhances seed germination and crop early growth for sustainable agriculture in Bangladesh

Biochar (BC) application to low-fertility soils enhances crop yield, soil quality, and sustainable agricultural production. Although many studies have explored the effects of biochar on tropical crops, research specific to Bangladesh is limited. Given the agrarian system in Bangladesh, dense population, and vulnerability to climate change, adopting sustainable agricultural practices is essential. This study evaluates the impact of different biochar dosages on the germination and early growth of five major crops Oryza sativa (rice), Triticum aestivum (wheat), Capsicum annuum (chili), Solanum melongena (eggplant), and Solanum lycopersicum (tomato) using Acacia auriculiformis wood-waste biochar. The research was conducted using a randomized complete block design (RCBD) in a nursery setting. Biochar treatments of 10 t/ha and 15 t/ha were applied, with assessments made of germination (%), germination rate (after 7 days), shoot height (cm), root height (cm), leaf number, and root-shoot dry weight ratio. The results indicated a significant (p < 0.001) increase in germination (%) with higher biochar application rates. The linear mixed-effects model showed a significant effect of biochar treatment on germination (%) (F = 57.33, p < 0.001) and a significant interaction with crop type (F = 15.84, p < 0.001). In C. annuum, the 15 t/ha treatment resulted in a 96% increase in germination compared to the control (43.3 ± 1.08% vs 85.1 ± 2.15%). Similarly, in O. sativa, germination was significantly higher with the 10 t/ha (84.5 ± 1.52%) and 15 t/ha (91.8 ± 1.49%) treatments compared to control (59.3 ± 2.38%). Biochar significantly (p < 0.05) influenced early germination rates (after 7 days) and early growth parameters (e.g., shoot length, leaf count, root-shoot ratio), with the 15 t/ha treatment showing substantial improvements for C. annuum and O. sativa, while no significant effects were observed for S. lycopersicum. These findings underscore the potential of A. auriculiformis in enhancing germination and early growth of economically important crops, highlighting its role in promoting sustainable agriculture in Bangladesh.

Bayesian optimized indoor positioning algorithm based on dual clustering

Abstract Wi-Fi indoor positioning provides a simple, convenient, ubiquitous and cost-effective solution by matching a pre-established Wi-Fi Received Signal Strength Indication (RSSI) fingerprint database with the RSSI values received from mobile terminals. However, due to the influence of the complex indoor environment on the signal, its accuracy can only reach the meter scale, and the huge fingerprint database leads to inefficient positioning. To solve this problem, the Canopy algorithm is used for coarse clustering, and then the K-means algorithm is used for fine clustering to determine the number of clusters and the initial clustering center to form multiple clustering sub-bases, which improves the positioning efficiency by about 95.05%. In the real-time matching stage, the sub-banks with the highest similarity are selected for matching by the correlation coefficient method, and combined with the Weighted K-Nearest Neighbors (WKNN) algorithm, this paper proposes an improved Bayesian probabilistic optimization algorithm, and the final experimental results show that the average positioning accuracy is improved by about 38.64%, the average runtime is shrunk by about 93.51%, and the stability of the system is slightly improved, which effectively improves the positioning accuracy, real-time performance, and stability.

Comparing color qualia structures through a similarity task in young children versus adults

Examination of the subjective qualitative aspects of an experience, or “qualia” in short, is a fundamental and core aspect of consciousness research. How can we characterize the particular quality of redness, i.e. a red quale? Based on a recent proposal of the structural characterization of qualia, which did not rely on verbal descriptions, we developed a task that obtained pairwise similarity judgments at four graded levels, with easy and intuitive visual interfaces designed to engage young children. We examined color qualia structures in children (3 to 12-y-old in Japan and 6 to 8-y-old in China) and compared these with those of Japanese adults. Approximately half of the assessed 3-y-old children completed the experiment via our touch panel device version of the task and had reliable responses. Despite known developmental and/or cultural effects of color term usage, we found that color qualia structures were quite similar across the age groups and cultures. Our finding supports the view that color qualia structures emerge early. We also observed age-related differences in the evaluations of some color pairs, which implied subtle changes in the structures behind color experience.

Electronic vascular conduit for in situ identification of hemadostenosis and thrombosis in small animals and nonhuman primates

The efficacy and safety of acetazolamide in chronic mountain sickness: A systematic review and meta‐analysis of randomized controlled trials

Objective The impact of acetazolamide (ACZ) in chronic mountain sickness (CMS) has not been fully assessed. The purpose of this systematic review is to evaluate the effectiveness and safety of acetazolamide in the treatment of chronic mountain sickness. Research methods This systematic review and meta-analysis were conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The primary outcome measure was CMS clinical score. Secondary outcomes included CMS total score,hematocrit (HCT), Pondus Hydrogenii‌ (pH), arterial oxygen pressure (PaO2), arterial carbon dioxide pressure (PaCO2), bicarbonate concentration (HCO3), and adverse events. Results Five randomized controlled trials were included, comprising a total of 137 subjects, with 78 in the acetazolamide group and 59 in the control group.The CMS clinical score showed an MD of −0.31 (95% CI, −1.13 to −0.51, P = 0.46),the results indicated no statistical significance.But the CMS total score had an MD of −1.13 [95% CI, −2.03 to −0.23], P = 0.01, showing a significant difference.The HCT results showed an MD of −2.70 (95% CI, −4.58 to −0.82; P = 0.005), indicating a statistically significant reduction. The result of PaO2,PaCO2,pH and HCO3 are statistically significant. In terms of adverse events, increased diuresis and headache were not statistically significant. Paresthesia had a significant difference. Conclusion Based on the available evidence, we conclude that ACZ 250 mg is a safe, reliable, and low-cost treatment option for chronic mountain sickness. By reducing HCT, PaCO2, pH, and HCO3, and increasing PaO2, it improves respiratory and circulatory parameters in CMS patients and effectively treats CMS.

Comparative pregnancy rate after colorectal resection versus other surgical procedures for deep infiltrating rectal endometriosis: a systematic review and meta-analysis

Identification of a ligand-binding site on tubulin mediating the tubulin–RB3 interaction

For decades, microtubules—composed of αβ-tubulin dimers—have been primary targets for cancer chemotherapy. While eight binding sites on the tubulin dimer have been structurally characterized, this study reveals a ninth. We found that the tubulin inhibitor Tumabulin-1 (TM1, a BML284 derivative) binds simultaneously to the well-known colchicine site and a previously unknown site, designated as Tumabulin site. This site resides at the interface of α1-tubulin, β1-tubulin, and RB3 within the tubulin–RB3–tubulintyrosine ligase complex. Remarkably, two TM1 molecules bind cooperatively to this relatively large pocket, interacting with all three proteins. Crucially, this binding is dependent on RB3; it is absent when RB3 is missing or the key residue H71 is mutated (H71Q). We further designed and synthesized Tumabulin-2 (TM2) that selectively binds the Tumabulin site, excluding binding the colchicine site. TM2 acts as a molecular glue, strengthening the interaction between RB3 and the tubulin dimer and consequently enhancing RB3’s tubulin-depolymerizing activity. In conclusion, our findings confirm the existence of a ninth tubulin-binding site and offer a promising foundation for developing Tubulin–RB3 molecular glues as a next generation of anticancer therapeutics.

Global characterization of mouse testis O-glycoproteome landscape during spermatogenesis

RETRACTED: Fischer’s ratio and DNA damage in hypoxemia-induced brain injury in rat model: prophylactic role of quercetin and mexamine supplementation

Hypoxemia brain injuries arise when the brain’s oxygen supply is restricted. Brain cells gradually die and become impaired as a result of the restricted oxygen flow a diversity of signaling pathways are involved in the pathophysiology of brain damage. One of the main concerns when examining the rate of protein breakdown is the measurement of the serum amino acid ratio. Valine, leucine, and isoleucine make up branched-chain amino acids, while phenylalanine and tyrosine make up aromatic amino acids. A vital tool for assessing the severity of hypoxemia is Fischer’s ratio. The goal of this article is to determine how quercetin (QUR) and/or mexamine (MEX) prevented synfat (SN)-induced brain damage in a rat models. It also aimed to elucidate the various cross-linked inflammatory pathways, DNA damage, and Fischer’s ratio. Following QUR and MEX therapy, synfat-induced hypoxemia. Hemoglobin (Hb) levels were markedly reduced by synfat-intoxication, and oxidative stress and inflammatory biomarkers, including TNF-??, MDA, interleukin-6 (IL-6), and C -reactive protein (CRP), were elevated. Hemoglobin levels, oxidative stress biomarkers, and the aberrant expression of pro-inflammatory cytokines were all altered by QUR and/or MEX therapy. Similarly, the concentration of γ-aminobutyric acid, serotonine, noradrenaline, and intropin in cerebral tissue is restricted. Similarly, the COMET assay and 8-oxo-7,8-dihydro-2’-deoxyguanosine analysis (8-oxodG) demonstrated that QUR and MEX potentially altered synfat-induced brain DNA damage. The results confirmed the potential impact of this combined strategy as a powerful therapy for brain hypoxemia, concluding that treatment via QUR with MEX was superior therapy in modulating synfat-triggered cerebral injury.

Carbon management in massive electric vehicle temporal and spatial scheduling with automotive electronic forensics

p53 activates circASCC3 to repress R-loops and enhance resistance to chemotherapy

The tumor suppressor p53 can trigger tumor resistance to chemotherapy by facilitating DNA damage repair and maintaining genomic integrity. Here, we report that a p53-induced circular RNA circASCC3 promotes chemotherapeutic resistance by resolving R-loops. Our results reveal that p53 directly activates the transcription of ASCC3 , the host gene of circASCC3. In addition, the RNA-binding protein SFPQ is identified to inhibit the formation of circASCC3 by associating with its flanking regions. Importantly, p53 facilitates the formation of circASCC3 by repressing the expression of SFPQ. CircASCC3 has a marginal effect on the survival and growth of cancer cells under normal growing conditions but surprisingly boosts their survival and growth in response to DNA damage stress. Mechanistic analysis reveals that circASCC3 binds to the DEAD-box RNA helicase DDX5 to inhibit its proteasomal degradation. This results in the prevention of R-loop accumulation due to DNA damage, thereby conferring tumor resistance to chemotherapy. Together, our study uncovers that p53 activates circASCC3 to promote R-loop resolution, which maintains genomic stability and potentially contributes to chemoresistance.

Surface darkening by abundant and diverse algae on an Antarctic ice cap

Abstract Algal blooms play important roles in physical and biological processes on glacial surfaces. Despite this, their occurrence and impacts within an Antarctic context remain understudied. Here, we present evidence of the large-scale presence, diversity and bioalbedo effects of algal blooms on Antarctic ice cap systems based on fieldwork conducted on Robert Island (South Shetland Islands, Antarctica). Algal blooms are observed covering up to 2.7 km2 (~20%) of the measured area of the Robert Island ice cap, with cell densities of up to 1.4 × 106 cells ml−1. Spectral characterisation reveal that these blooms increase melting of the ice cap surface, contributing up to 2.4% of total melt under the observed conditions. Blooms are composed of typical cryoflora taxa, dominated by co-occurring Chlorophyceae, Trebouxiophyceae, and Ancylonema. However, morphological variation and genetic diversity in Ancylonema highlight the influence of regional endemism and point to a large and under-characterised diversity in Antarctic cryoflora.

Boosting recovery before surgery: The impact of prehabilitation on upper gastrointestinal cancer patients – A quantitative comparative analysis

Background Emerging research presents divergent perspectives on the efficacy of prehabilitation for patients scheduled for surgery due to upper gastrointestinal (GI) cancers, capturing the attention of both the scientific community and surgical professionals. This quantitative comparative analysis seeks to assess the association of prehabilitation to ameliorate postoperative outcomes in individuals with upper GI cancers, thereby providing a comprehensive evaluation of its potential benefits within a surgical context. Materials and methods Medline, Embase, Cochrane Library and Web of Science were searched up to February 2024. Studies reporting the association between prehabilitation, and postoperative complications, readmissions or other outcomes of interest were included. Fixed or random effect models were used, and forest plots were applied to show the results of the quantitative comparative analysis. Results A total of 198 studies were initially screened based on titles and abstracts, with 129 studies subsequently excluded. Overall, 69 full-text studies were identified, of which 12 studies were finally included for qualitative analysis in the quantitative comparative analysis after determining whether the inclusion and exclusion criteria were met. The pooled results indicated that prehabilitation significantly reduced the overall postoperative complication rates in patients with upper GI cancer undergoing surgical therapy with the pooled OR of 0.59 (95%CI: 0.39–0.88). Moreover, prehabilitation was also shown to be a protective factor of pulmonary complications (OR: 0.54, 95%CI: 0.36–0.80) and ICU readmissions (OR: 0.23, 95%CI: 0.06–0.89). Conclusion The correlation between prehabilitation and a reduction in overall postoperative complications, pulmonary complications, and ICU readmissions among patients with upper GI cancer is substantiated by significant data. This pivotal finding necessitates further empirical investigation to validate these initial results and ascertain the clinical efficacy of prehabilitation protocols, thereby informing future surgical practice strategies.

Population genomic analysis identifies the complex structural variation at the fibromelanosis (FM) locus in chicken

Abstract Phenotypic diversity and its genetic basis are central questions in biology, with domesticated animals offering valuable insights due to their rapid evolution the last 10,000 years. In chickens, fibromelanosis (FM) is a striking pigmentation phenotype characterized by hyperpigmentation. A previous study identified a complex structural variant involving both two large duplications (127.4 and 170.5 kb in size) and inversions associated with upregulated expression of the Endothelin 3 (EDN3) gene. However, the detailed organization of the structural arrangements have remained unclear. In this study, we conducted a comprehensive genomic survey of 517 FM chickens representing 44 different populations. Our results elucidate the complex arrangement of the duplications and inversions at the FM locus based on the large-scale genomic survey, population level genotyping, and linkage disequilibrium analysis, providing conclusive support for one specific configuration of the two large duplications, resolving a controversy that has been unresolved for more than a decade. Our results show that the birth of this complex structural variant must have involved an interchromosomal rearrangement creating fixed heterozygosity due to sequence differences between the two copies of the 127.4 kb duplication. This study shows how population genomics can be used to understand complex structural variations that underlie phenotypic variation.